The invention generally relates to systems and methods for on-line reaction monitoring. In certain embodiments, the invention provides systems that include a reaction vessel having an outlet, a quantitation unit coupled to the outlet and configured to introduce internal standard and solvent into reaction solution flowed from the reaction vessel, one or more ion generating devices that receive flow from the quantitation unit, and a mass spectrometer. In certain embodiments, the invention provides systems for multiple reaction monitoring that include a plurality of reaction vessels, a plurality of ion generating devices, a plurality of channels, each channel coupling a reaction vessel to an ion generating device, an actuator coupled to the plurality of ion generating devices to thereby allow movement of the plurality of ion generating devices, and a mass spectrometer.

Set forth herein are glycopeptide biomarkers useful for diagnosing diseases and conditions, such as but not limited to, cancer (e.g., ovarian), an autoimmune disease, fibrosis and aging conditions. Also set forth herein are methods of generating glycopeptide biomarkers and methods of analyzing glycopeptides using mass spectroscopy. Also set forth herein are methods of analyzing glycopeptides using machine learning algorithms.

A method of performing targeted multiplexed mass spectrometry includes performing, at a mass spectrometer, a targeted MS3 analysis of an isobaric tag-labeled target analyte included in a multiplex sample eluting from a column. The targeted MS3 analysis is performed during an acquisition segment scheduled based on an expected retention time of the isobaric tag-labeled target analyte. The method further includes performing, during the acquisition segment, a plurality of MS2 analyses of product ions derived from components included in the multiplex sample and eluting from the column. The method further includes determining, based on MS3 mass spectra acquired by the targeted MS3 analysis and MS2 mass spectra acquired by the plurality of MS2 analyses, a relative quantity of the isobaric tag-labeled target analyte in the multiplex sample.

Methods for identifying and determining an abundance of an alpha fetoprotein (AFP) glycoform in a biological sample includes obtaining a biological sample, separating AFP from the biological sample as an enriched AFP sample, separating intact AFP from the enriched AFP sample, subjecting the intact AFP to high resolution mass spectrometry to generate a mass spectrum, identifying at least one AFP glycoform from the mass spectrum, and determining an abundance of the at least one AFP glycoform in the biological from the mass spectrum.

Isobaric mass spectrometry tags (e.g., TMT) are susceptible to ratio compression, which arises from the co-isolation and co-fragmentation of interfering species that also contribute to the final reporter ion ratios. Additional stages of ion activation/transformation (e.g., MSn and PTR) have been shown to decrease ratio compression. Embodiments of the present invention include a mass spectrometry cleavable moiety on the isobaric mass tags. The cleavable moiety allows for a predictable mass loss, and results in an improved tag reporter ion purity.

A method of analysis using mass spectrometry and/or ion mobility spectrometry is disclosed. The method comprises: using a first device to generate smoke, aerosol or vapour from a target comprising or consisting of a microbial population; mass analysing and/or ion mobility analysing said smoke, aerosol or vapour, or ions derived therefrom, in order to obtain spectrometric data; and analysing said spectrometric data in order to analyse said microbial population.

The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.

A method for deconvoluting measured mass spectrometry data, the method comprising: receiving measured mass spectrometry data representing at least two molecular moieties each having a respective isotopic pattern, wherein at least two of said isotopic patterns overlap; iteratively filling a set of mass channels to produce an approximated version of the mass spectrometry data, said iterative filling comprising a number of iterations, each iteration comprising filling one or more of the mass channels with a chunk of intensity data according to the isotopic pattern of a respective one of the two or more molecular moieties selected for said iteration; terminating said iterative filling when a fitness criterion is met indicating a fit of the approximated version of the mass spectrometry data to the measured mass spectrometry data; and determining the amount of each molecular moiety that produced the measured mass spectrometry data based on the total amount of fills according to the respective isotopic pattern of said molecular moiety.

The present technology relates to a method of analyzing a sample including an analyte. The method includes injecting the sample including the analyte into a mobile phase. The mobile phase includes a metal chelator additive having a concentration between about 1 ppm to about 10 ppm. The method also includes separating the analyte using liquid chromatography and analyzing the analyte using a mass spectrometer, an ultra-violet detector, or a combination thereof.

Disclosed herein is a method of determining whether a subject has or is at risk of developing a cancer. The method comprises, obtaining a sample from the subject; determining the levels of at least two target polypeptides, which are selected from the group consisting of, ANXA2, HSPA5, KNG1 and MMP1; and assessing whether the subject has or is at risk of developing the cancer based on the levels of target polypeptides. The present method provides a potential means to diagnose and predict the occurrence of oral squamous cell carcinoma, and accordingly, the subject in need thereof could receive a suitable therapeutic regimen in time.